Allow stratified output from picrust2

[hh1985]

Description of feature

Please add option to enable stratified results output from picrust2:--stratified and related flags.

[hh1985]

BTW, to add more parameters, is there any way to update the parameter file somewhere directly instead of downloading the source code and manually changing the configuration of the pipeline?

[erikrikarddaniel]

BTW, to add more parameters, is there any way to update the parameter file somewhere directly instead of downloading the source code and manually changing the configuration of the pipeline?

Yes, to add --stratified you can create a config file (typically nextflow.config in the directory in which you're running the pipeline) looking like this:

process {
  withName: PICRUST {
        ext.args = "-t epa-ng --remove_intermediate --stratified"
  }
}

[erikrikarddaniel]

This technique allows full freedom to end users to set parameters to programs exactly as they want them instead of waiting for a developer to add a flag to the pipeline. If you're satisfied with this, please close the issue.

[hh1985]

That's exactly what I want. Thanks!